At the beginning of Episode II, there's an assassination attempt on senator Amidala's life. Shortly after, a few members of the Jedi council and some politicians have a meeting, with Padme suggesting that Dooku was behind the attack.

2 Answers
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There's some more elaboration in the film's official novelisation. In short, Dooku is a known associate of Nute Gunray, a deeply disreputable character as far as Padmé's people are concerned (he's the guy who arranged the blockade and invasion of their world). On top of that, there seem to be a wide number of assassination attempts going on of people who're known to oppose Dooku's political objectives. She adds up 2 and 2 and gets 4.

“The separatists have shown themselves not to be above violence,” he explained. “There have been assassination attempts across the Republic.”

“But wouldn’t Count Dooku and the separatists consider Senator Amidala almost an ally at this time?” Captain Typho interjected, and both Panaka and Padmé looked at the usually quiet man in surprise.

Padmé’s look quickly turned into a stare; there was an angry edge to
her fair features. “I am no friend to any who would dissolve the
Republic, Captain,” she insisted, her tone leaving no room for
debate and of course, there would be no debating that point. In the
few years she had been a Senator, Amidala had shown herself to be
among the most loyal and powerful supporters of the Republic, a
legislator determined to improve the system, but to do so within the
framework of the Republic’s constitution. Senator Amidala fervently
believed that the real beauty of the governing system was its built-in
abilities, even demands, for self-improvement.

Note that her fellow senators also instantly suspect Separatists forces.

Ask Aak, Orn Free Taa, and Darsana, on their floating platforms down
by the podium, exchanged nervous glances as the cheers and boos echoed
about the great hall. The fact that Amidala had just survived an
assassination attempt and yet was here begging the Senate to put off
raising an army against the likely perpetrators only added strength to
her argument, only elevated Amidala higher in the eyes of many and the
former Queen of Naboo, having stood firm against the Trade Federation
a decade before, was already held in high esteem by many. At Ask Aak’s
nod, Orn Free Taa demanded the floor, and was given it promptly by
Palpatine.

@Charles - The idea behind the Star Wars universe is that you can always dig deeper. The movie contains multiple references to things that were only explained in the books and the books contain references to things you can only understand by reading the various factbooks, etc. It's like a 50+ year-long treasure hunt.
– ValorumNov 29 '18 at 0:05

Her Ladyship likely knew that Confederacy of Independent Systems (CIS) leaders, stood to gain from her political demise; mostly in terms of easy tyranny for the CIS. She was not their only target, as the CIS intended the downfall of all democracy; essentially to make slave-labor easier to keep and harder-to-regulate (an advantage from the vantage of CIS slave-owners).

The seperatists' OOMs war-robots are sourced from Geonosis.
Notably, frontal assualts are a waste of troopers, as it's like standing outside an arms-dealer window, strategically.
... with similar attempts on Hypori: